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OPENSEQ.org
1JIW_PI
Genes: A B A+B
Length: 470 106 567
Sequences: 159 104 55
Seq/Len: 0.34 0.98 0.1
MirrorTree (Pazo et al. 2001) 0.65
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.07 0.03 0.09
2 0.07 0.03 0.09
5 0.07 0.03 0.10
10 0.07 0.03 0.10
20 0.07 0.03 0.10
100 0.09 0.06 0.10
∞ 0.17 0.08 0.10
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
283_V 54_L 1.59 0.23 0.00
228_G 50_L 1.46 0.19 0.00
340_L 64_T 1.41 0.17 0.00
265_T 68_I 1.37 0.17 0.00
307_E 8_A 1.32 0.15 0.00
8_Q 53_W 1.30 0.14 0.00
292_L 60_A 1.29 0.14 0.00
375_T 12_A 1.28 0.14 0.00
316_L 68_I 1.26 0.14 0.00
421_D 74_G 1.25 0.14 0.00
254_T 80_L 1.25 0.13 0.00
266_E 74_G 1.23 0.13 0.00
346_A 28_L 1.23 0.13 0.00
383_E 32_D 1.22 0.13 0.00
378_Y 46_D 1.20 0.12 0.00
120_G 79_M 1.20 0.12 0.00
379_G 17_L 1.20 0.12 0.00
373_A 50_L 1.19 0.12 0.00
388_A 54_L 1.18 0.12 0.00
444_A 7_S 1.16 0.12 0.00
292_L 53_W 1.16 0.12 0.00
109_I 8_A 1.16 0.11 0.00
441_G 80_L 1.15 0.11 0.00
87_A 72_E 1.13 0.11 0.00
225_D 62_R 1.13 0.11 0.00
228_G 62_R 1.13 0.11 0.00
271_S 12_A 1.13 0.11 0.00
164_P 89_Y 1.12 0.11 0.00
212_S 89_Y 1.12 0.11 0.00
237_D 89_Y 1.12 0.11 0.00
378_Y 73_R 1.12 0.11 0.00
378_Y 32_D 1.12 0.11 0.00
286_A 80_L 1.10 0.10 0.00
51_G 53_W 1.10 0.10 0.00
364_A 54_L 1.07 0.10 0.00
115_G 103_R 1.06 0.10 0.00
236_L 72_E 1.06 0.10 0.00
107_T 66_A 1.06 0.10 0.00
392_L 66_A 1.06 0.10 0.00
397_S 100_V 1.05 0.09 0.00
46_W 81_L 1.05 0.09 0.00
266_E 59_R 1.05 0.09 0.00
364_A 50_L 1.04 0.09 0.00
85_F 45_G 1.04 0.09 0.00
435_D 70_L 1.03 0.09 0.00
435_D 1_S 1.02 0.09 0.00
94_A 24_A 1.02 0.09 0.00
254_T 62_R 1.01 0.09 0.00
139_L 99_L 1.01 0.09 0.00
152_Y 99_L 1.01 0.09 0.00
217_W 12_A 1.01 0.09 0.00
128_S 99_L 1.01 0.09 0.00
18_R 89_Y 1.01 0.09 0.00
104_S 76_L 1.01 0.09 0.00
14_H 12_A 1.00 0.09 0.00
459_L 62_R 1.00 0.09 0.00
457_I 6_L 1.00 0.09 0.00
429_Q 78_L 1.00 0.09 0.00
109_I 9_S 0.98 0.08 0.00
235_L 43_L 0.98 0.08 0.00
282_S 39_S 0.98 0.08 0.00
275_S 54_L 0.97 0.08 0.00
457_I 81_L 0.97 0.08 0.00
193_G 12_A 0.97 0.08 0.00
111_F 2_S 0.96 0.08 0.00
192_A 2_S 0.96 0.08 0.00
425_G 2_S 0.96 0.08 0.00
404_L 95_D 0.96 0.08 0.00
328_V 28_L 0.96 0.08 0.00
310_L 66_A 0.96 0.08 0.00
226_F 96_G 0.96 0.08 0.00
85_F 55_P 0.96 0.08 0.00
59_Y 55_P 0.95 0.08 0.00
320_V 50_L 0.94 0.08 0.00
327_T 86_E 0.94 0.08 0.00
443_L 101_L 0.94 0.08 0.00
434_Y 99_L 0.94 0.08 0.00
6_Y 1_S 0.94 0.08 0.00
293_D 26_C 0.94 0.08 0.00
296_G 26_C 0.94 0.08 0.00
39_I 55_P 0.94 0.08 0.00
226_F 10_D 0.94 0.08 0.00
258_V 74_G 0.94 0.08 0.00
128_S 78_L 0.94 0.08 0.00
442_S 79_M 0.93 0.08 0.00
283_V 30_L 0.93 0.07 0.00
104_S 51_T 0.93 0.07 0.00
122_L 80_L 0.93 0.07 0.00
408_D 80_L 0.93 0.07 0.00
393_R 85_G 0.93 0.07 0.00
210_A 99_L 0.93 0.07 0.00
327_T 14_Q 0.92 0.07 0.00
89_S 12_A 0.92 0.07 0.00
235_L 81_L 0.92 0.07 0.00
316_L 8_A 0.91 0.07 0.00
407_L 102_R 0.91 0.07 0.00
10_D 23_P 0.91 0.07 0.00
293_D 3_L 0.91 0.07 0.00
296_G 3_L 0.91 0.07 0.00
110_H 76_L 0.91 0.07 0.00
235_L 6_L 0.91 0.07 0.00
101_Q 63_P 0.90 0.07 0.00
231_S 48_A 0.90 0.07 0.00
133_G 64_T 0.90 0.07 0.00
188_G 41_Y 0.90 0.07 0.00
142_V 76_L 0.90 0.07 0.00
389_P 53_W 0.90 0.07 0.00
125_G 43_L 0.90 0.07 0.00
378_Y 69_A 0.90 0.07 0.00
27_H 32_D 0.90 0.07 0.00
393_R 55_P 0.90 0.07 0.00
138_F 14_Q 0.90 0.07 0.00
272_A 46_D 0.90 0.07 0.00
127_F 32_D 0.89 0.07 0.00
245_L 70_L 0.89 0.07 0.00
388_A 89_Y 0.89 0.07 0.00
364_A 89_Y 0.89 0.07 0.00
29_S 83_R 0.88 0.07 0.00
26_G 83_R 0.88 0.07 0.00
217_W 32_D 0.88 0.07 0.00
122_L 62_R 0.88 0.07 0.00
297_F 99_L 0.88 0.07 0.00
340_L 78_L 0.88 0.07 0.00
385_S 76_L 0.88 0.07 0.00
401_K 26_C 0.88 0.07 0.00
30_Y 22_A 0.88 0.07 0.00
362_L 82_G 0.87 0.07 0.00
424_A 76_L 0.87 0.07 0.00
233_A 74_G 0.87 0.07 0.00
264_N 80_L 0.87 0.07 0.00
118_D 6_L 0.87 0.07 0.00
282_S 46_D 0.87 0.07 0.00
62_L 71_L 0.87 0.07 0.00
276_S 93_K 0.87 0.07 0.00
406_G 64_T 0.86 0.07 0.00
361_G 6_L 0.86 0.07 0.00
357_I 12_A 0.86 0.07 0.00
435_D 78_L 0.86 0.07 0.00
391_T 79_M 0.86 0.07 0.00
206_E 10_D 0.86 0.07 0.00
95_Q 89_Y 0.86 0.07 0.00
339_L 80_L 0.85 0.07 0.00
459_L 80_L 0.85 0.07 0.00
217_W 101_L 0.85 0.07 0.00
440_A 79_M 0.85 0.07 0.00
325_G 35_V 0.85 0.07 0.00
195_G 12_A 0.85 0.07 0.00
444_A 4_I 0.85 0.07 0.00
94_A 72_E 0.85 0.07 0.00
104_S 68_I 0.85 0.07 0.00
393_R 90_R 0.85 0.06 0.00
114_A 74_G 0.84 0.06 0.00
155_N 83_R 0.84 0.06 0.00
173_T 2_S 0.84 0.06 0.00
401_K 3_L 0.84 0.06 0.00
100_L 68_I 0.84 0.06 0.00
108_N 80_L 0.84 0.06 0.00
424_A 34_E 0.84 0.06 0.00
41_R 2_S 0.84 0.06 0.00
283_V 25_I 0.84 0.06 0.00
62_L 64_T 0.84 0.06 0.00
100_L 74_G 0.83 0.06 0.00
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
ID Seq/Len Name Options I_Prob Status
7386 0.1 1JIW_PI Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
4081 0.11 info 1JIW_PI E 1AKL_A Alkaline metalloproteinase 2RN4_A(1) Proteinase inhibitor Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4071 0 info 1JIW_PI E 1AKL_A Alkaline metalloproteinase 2RN4_A(1) Proteinase inhibitor Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
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